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VCell solver release: NFsim_x64 archives, image + SIF, v0.2.0 - #1

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Sep 30, 2026
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VCell solver release: NFsim_x64 archives, image + SIF, v0.2.0#1
jcschaff merged 8 commits into
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release/executables-and-image

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@jcschaff jcschaff commented Sep 30, 2026 •
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Implements PR A4 of VCell's solver-repo plan (docs/plan-solver-repos.md on VCell master): this repo now meets the solver-release contract (§1) next to its existing Python wheels. Details in the new SOLVER-RELEASE.md.

What changes

  • NFsim_x64 target — NFsim with VCell's main (VCell/src/VCellNFSim.cpp, already in the repo but not built): [[[progress]]] markers on stdout, and with -DOPTION_VCELL_MESSAGING=ON status messages to VCell's broker for a trailing -tid <n> (broker read from the input's <jms> element), as the legacy vcell-solvers build did. Vendors VCellMessaging (from vcell-fvsolver) and vcommons (from vcell-solvers). The plain NFsim target and the Python binding are unchanged.
  • Release workflow (.github/workflows/release.yml), on PRs / main / v* tags:
    • linux64.tgz, linux64arm.tgz: built on manylinux_2_28 in Docker, messaging ON, with a minimal HTTP-only libcurl linked statically. The build fails if anything beyond glibc/libstdc++/libgcc_s gets linked.
    • mac64.tgz: universal arm64+x86_64, ad-hoc signed, only /usr/lib dependencies.
    • win64.zip: MinGW-w64 gcc, fully static, with only Windows system DLLs (the legacy build was MinGW too; MSVC left NFsimMain unresolved at link time).
    • Each archive holds NFsim_x64[.exe], LICENSE, LICENSE-GPL-3.0.txt and VERSION.
    • Image ghcr.io/virtualcell/vcell-nfsim (amd64+arm64, debian:bookworm-slim runtime) and SIF vcell-nfsim_singularity (amd64), tagged :X.Y.Z on tags and :latest + :sha-* on main.
    • On a tag, the GitHub release gets the archives, the wheels + sdist (publish-python-package.yml is now also workflow_call; its manual dispatch still works) and SHA256SUMS.
  • Standard entrypoint /usr/local/bin/vcell-solver-entrypoint: help → exit 0, NFsim_x64 … → exec, anything else → exit 2. It writes nothing and runs as any uid.
  • Messaging fix: SimulationMessaging's messaging constructor left bStopRequested uninitialized. A garbage true made the solver exit without waiting for the messaging thread, so JOB_COMPLETED was sometimes never sent. CI caught it, and the fix is in VCell/messaging. The same code is in vcell-fvsolver's and vcell-solvers' VCellMessaging.
  • Version 0.2.0.

Checks

  • Smoke test tests/container/smoke.sh: the committed reference model through Docker (uid 12345, bind mount) and through the SIF under apptainer run --containall (non-root). Argv matches SlurmProxy's (/simdata, -tid 0), and the input's broker is pointed at a local fake broker. Outputs must be byte-identical to tests/smoke/*.expected, and JOB_STARTING + JOB_COMPLETED must reach the broker.
  • Equivalence tests/equivalence/compare_legacy.sh: 5 seeds through the legacy vcell-solvers v0.0.44-dev4 NFsim_x64 and the new one, compared byte for byte. In CI it is byte-identical on linux64, on both mac64 slices (arm64 native, x86_64 under Rosetta), and on win64 against the legacy v0.0.40 NFsim_x64.exe that VCell's Windows desktop ships.

Decisions

  • Messaging is ON for the Linux archives and the image (one binary for desktop and HPC; without -tid it behaves like the desktop binary). mac and Windows stay messaging OFF, like the legacy desktop binaries.
  • libcurl is linked statically as an HTTP-only build, so there is nothing to bundle. The broker URL is plain http://host:port.
  • NFsim's GPL-3.0 text ships as LICENSE-GPL-3.0.txt next to the repo's MIT LICENSE.
  • The archive VERSION comes from the tag / pyproject.toml. The repo's top-level VERSION file belongs to BioNetGen, so it is left alone.

🤖 Generated with Claude Code

jcschaff and others added 8 commits September 30, 2026 11:29
@jcschaff @claude
Build NFsim_x64, the VCell-facing executable, with optional VCell mes…
0ff0ff1 
…saging

NFsim_x64 is NFsim with VCell's main (VCell/src/VCellNFSim.cpp, previously unbuilt here):
[[[progress]]] markers on stdout and, with -DOPTION_VCELL_MESSAGING=ON, status messages to
VCell's broker for a trailing -tid <n>, as the legacy vcell-solvers build did. Vendors the
VCellMessaging library (from vcell-fvsolver) and the vcommons helpers it needs (from
vcell-solvers). The plain NFsim target and the Python binding are unchanged; NFsim_x64 is
skipped under scikit-build.

Also: honour a caller-set CMAKE_OSX_ARCHITECTURES (universal builds) and pass -m64 only on
x86_64 (aarch64 gcc rejects it).

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
@jcschaff @claude
Linux packaging, solver image with the standard entry point, smoke an…
fcbe6c6 
…d equivalence tests

- packaging/build-linux.sh: NFsim_x64 on manylinux_2_28, messaging ON, minimal HTTP-only
  libcurl linked statically; fails if anything beyond glibc/libstdc++/libgcc_s is linked.
- docker/Dockerfile: build stage = the archive's contents, an "archive" stage exporting
  linux64.tgz / linux64arm.tgz, and a debian:bookworm-slim runtime with them on PATH.
- docker/entrypoint.sh: /usr/local/bin/vcell-solver-entrypoint (help -> 0, NFsim_x64 -> exec,
  else -> 2); writes nothing, any uid, read-only SIF.
- tests/container/smoke.sh + fake_broker.py: the reference model through an image as
  SlurmProxy runs it (/simdata, -tid 0), byte-exact against tests/smoke/*.expected, and the
  status messages must reach the (fake) broker.
- tests/equivalence/compare_legacy.sh: five seeds through the legacy vcell-solvers
  v0.0.44-dev4 NFsim_x64 and the new one, byte-for-byte.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
@jcschaff @claude
Release workflow: executable archives, image + SIF, GitHub release wi…
66b198e 
…th wheels; v0.2.0

release.yml builds linux64/linux64arm (Docker, manylinux_2_28), mac64 (universal, ad-hoc
signed) and win64 (MSVC, static runtime) archives, smoke-tests the image (Docker as a
non-root uid, and the SIF under apptainer --containall, both with -tid), compares with the
legacy binary, publishes ghcr.io/virtualcell/vcell-nfsim (multi-arch) and
vcell-nfsim_singularity (amd64 SIF) on main and tags, and on a vX.Y.Z tag creates the
release with the archives, the wheels + sdist (publish-python-package.yml, now also
workflow_call) and SHA256SUMS. SOLVER-RELEASE.md documents the contract; version 0.2.0.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
@jcschaff @claude
Fix the Windows build (NOMINMAX) and the mac dependency check (skip o…
d8c562d 
…tool's per-arch headers)

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
@jcschaff @claude
Windows: build NFsim_x64 with MinGW-w64, fully static; fix the glibc-…
c148622 
…2.28 check (NFsim -help exits 255)

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
@jcschaff @claude
Windows: compare with the legacy v0.0.40 NFsim_x64.exe VCell's deskto…
a4aa168 
…p ships

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
@jcschaff @claude
Messaging: initialize bStopRequested in the messaging constructor
e2fbf9f 
It was left uninitialized in the SimulationMessaging(broker, ...) constructor, so a garbage
non-zero value made nfsimExit skip waitUntilFinished(): the process could exit before the
messaging thread posted JOB_COMPLETED (seen in CI: JOB_STARTING reached the broker, the
completion never did). Also return from lockMessaging() on POSIX. The same code is in
vcell-fvsolver's and vcell-solvers' VCellMessaging.

The smoke test takes BROKER_HOST (default 127.0.0.1) for runs where the solver sees the host
under another name (host.docker.internal on Docker Desktop).

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
@jcschaff @claude
Smoke test: capture the help text instead of piping it into grep -q (…
b7e4a09 
…SIGPIPE under pipefail)

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
@jcschaff
jcschaff merged commit 098fa51 into main Sep 30, 2026
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